Metadata-Version: 2.1
Name: genice_twist
Version: 0.1.2
Summary: Twist analysis plugin for GenIce.
Home-page: https://github.com/vitroid/genice-twist/
Author: Masakazu Matsumoto
Author-email: vitroid@gmail.com
License: MIT
Description: # [genice-twist](https://github.com/vitroid/genice-twist/)
        
        Draw the structure with twist order parameter.
        
        version 0.1.2
        
        ## Requirements
        
        * genice<2.0
        * genice-svg>=0.4
        * twist-op>=0.2
        * sklearn
        
        ## Installation from PyPI
        
            % pip install genice_twist
        
        ## Manual Installation
        
        ### System-wide installation
        
            % make install
        
        ### Private Installation
        
        Copy the files in formats/ into your local formats/ folder.
        
        ## Usage
        
            
            usage:
                genice II -f twist[options:separated:by:colons] > file
            
            Output the twist values for all the hydrogen-bonded pairs.
            
            options:
                png      Draw the hydrogen bonds with a rainbow palette according to the twist value in PNG format.
                png:CM   Draw the hydrogen bonds with color-mixing scheme in PNG format.
                png:DB   Draw the hydrogen bonds with decision-boundary coloring scheme in PNG format.
                png:SB   Draw the hydrogen bonds with simple boundary coloring scheme in PNG format.
                svg      Draw the hydrogen bonds with a rainbow palette according to the twist value in SVG format.
                svg:CM   Draw the hydrogen bonds with color-mixing scheme in SVG format.
                svg:DB   Draw the hydrogen bonds with decision-boundary coloring scheme in SVG format.
                svg:SB   Draw the hydrogen bonds with simple boundary coloring scheme in SVG format.
                yaplot   Draw the hydrogen bonds with a rainbow palette according to the twist value in YaPlot format.
                shadow   Draw shadows to the atoms (PNG and SVG)
                Ih=filename.twhist   Specify the (two-dimensional) histogram of twist parameter in pure ice Ih.
                Ic=filename.twhist   Specify the (two-dimensional) histogram of twist parameter in pure ice Ic.
                LDL=filename.twhist  Specify the (two-dimensional) histogram of twist parameter in pure LDL.
                HDL=filename.twhist  Specify the (two-dimensional) histogram of twist parameter in pure HDL.
                rotatex=30   Rotate the picture (SVG and PNG)
                rotatey=30   Rotate the picture (SVG and PNG)
                rotatez=30   Rotate the picture (SVG and PNG)
        
        ## Auxiliary Files
        
        * IhST2.twhist
        * IcST2.twhist
        * LDLST2.twhist
        * HDLST2.twhist
        
        They are two-dimensional (i.e. real and imaginary) histograms of twist order parameter of ST2 water at 235 K, 0.98 g cm$^{-3}$. You have to prepare the appropriate histogram if you want to apply CM (color-mixing) or DB (decision-boundary) coloring scheme to other water models or in other conditions.
        
        ## Test in place
        
            % make test
        
        ## Reference
        
        * Matsumoto, M., Yagasaki, T. & Tanaka, H. A Bayesian approach for identification of ice Ih, ice Ic, high density, and low density liquid water with a torsional order parameter. J. Chem. Phys. 150, 214504 (2019).
        
Keywords: genice,chirality
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.5
Description-Content-Type: text/markdown
